Recognition of transcription factors in complex with operator DNA at atomic resolution

Abstract

In this mini-review we have presented our common opinion on one of the key problems of molecular biology and very possibly “molecular medicine”. Since the early nineties of last century many significant works have been published on the atomic structure of complexes of transcription factor with DNA-fragments in the form of double-helix, which exist in the cell media. To this time, a few reviews have appeared and we have also finished our study of protein-DNA binding interactions of such complexes. By analyzing numerous significant structural data we have deduced the recognition rules which allow understanding the general feature of such interactions for most wide-spread families of two widespread classes of transcription factors: homeodomains and Zn-fingers. In these cases, we have concentrated only on the main more significant sort of binding DNA-region - its major groove. As the results show, we have deduced several common regularities of these protein-DNA bindings. We have shown that the common type of binding of factor-DNA is determined by the groups of invariant binding contacts while the particular feature of any definite transcription factor is determined by the group of variable contacts.